Cell cycle phase prediction
add_cell_cycle.RdPredict cell cycle phase
Usage
add_cell_cycle(
sobj,
assay = "RNA",
species_rdx = NULL,
cc_pairs = NULL,
cc_genes = NULL,
BPPARAM = NULL,
nbin = 24,
my_seed = 1337L,
verbose = FALSE
)Arguments
- sobj
A Seurat object
- assay
CHARACTER : name of the assay corresponding to the initial input data (default to 'RNA')
- species_rdx
CHARACTER : a character string, such as 'mm' or 'hs', representing the species studied in sobj (no default)
- cc_pairs
LIST : a list of three vectors (G1, S, G2M) containing genes pairs associated with G1-phase, S-phase and G2M-phase, used in cell-cycle regression by scran::cyclone (default to the internal dataset)
- cc_genes
LIST : a list of two vectors (s.genes and g2m.genes) containing genes associated with S-phase and G2M-phase, used in cell-cycle regression by Seurat::CellCycleScoring (default to the internal dataset)
- BPPARAM
an object of class DoparParam to be passed to BPPARAM parameter of scran::cyclone function. Could be generate by our create.parallel.instance function
- nbin
INTEGER : number of bins of aggregate expression levels for all analyzed features, to be passed to Seurat::CellCycleScoring function (default to 24)
- my_seed
INTEGER : random seed (default to 1337L)
- verbose
LOGICAL : whether to print progress bars and output messages or not (default to FALSE)